framed 0.3.1

framed - metabolic modeling for python

framed is a python package for analysis and simulation of metabolic models. The main focus is to provide support for different modeling approaches.

• Modeling: Constraint-based models, Kinetic models, Bioprocess models

• I/O: Import/Export from SBML and/or plain text formats

• Solver support: Gurobi, CPLEX, GLPK

• COBRA tools:

  • Simulation: FBA, pFBA, loopless-FBA, MOMA, linearMOMA, ROOM

  • Analysis: FVA, gene essentiality, PhPP, flux envelope plots

  • Omics integration: GIMME, E-Flux

  • Strain design: brute force, hill climbing

• Kinetic tools:

  • Time-course and steady-state simulation

  • Parameter and flux sampling

  • Calibration from metabolomics data

• Bioprocess modeling: Dynamic FBA (single and multi-species)

Documentation

For documentation and API please check: http://framed.readthedocs.io/

Instalation

pip install framed

Credits and License

Developed at:

• The Novo Nordisk Fundation Center for Biosustainability (2013)

• Centre of Biological Engineering, University of Minho (2014-2015)

• European Molecular Biology Laboratory (2016)

Released under an Apache License.